SC_ROI

Spinal cord ROI ¹ drawing tool

Dependency

Python 2.7

• numpy
• matplotlib (>= 1.5 works but GUI was optimized on version 2.0)
• nibabel

python-tk:

• Ubuntu/Debian: sudo apt-get install python-tk
• Fedora: yum install tkinter

Installation

We don't have any fancy installation method yet.

1. Download to any directory: git clone git@github.com:junqianxulab/SC_ROI.git
2. Give executable permission to the main file: chmod +x {download_directory}/SC_ROI/draw_sc_roi/draw_sc_roi.py
3. Make a symbolic link in a user directory (e.g. ln -s {download_directory}/SC_ROI/draw_sc_roi/draw_sc_roi.py ${HOME}/bin) or a system directory (e.g. ln -s {download_directory}/SC_ROI/draw_sc_roi/draw_sc_roi.py /local/bin).

• Note that the directory containing the symbolic link should be in a PATH environment.

4. Try draw_sc_roi.py

Documentation

• Manual

under construction

References

Footnotes

1. Xu et al., Improved in vivo diffusion tensor imaging of human cervical spinal cord, NeuroImage, 2013 ↩